318 results on '"Scientific Correspondence"'
Search Results
2. A rare case of paediatric astroblastoma with concomitant MN1-GTSE1 and EWSR1-PATZ1 gene fusions altering management
- Author
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Chadda, Karan R., Holland, Katherine, Scoffings, Daniel, Dean, Andrew, Pickles, Jessica C., Behjati, Sam, Jacques, Thomas S., Trotman, Jamie, Tarpey, Patrick, Allinson, Kieren, Murray, Matthew J., Genomics England Research Consortium, Pickles, Jessica C [0000-0001-7888-1723], Jacques, Thomas S [0000-0002-7833-2158], Murray, Matthew J [0000-0002-4480-1147], Apollo - University of Cambridge Repository, Pickles, Jessica C. [0000-0001-7888-1723], Jacques, Thomas S. [0000-0002-7833-2158], and Murray, Matthew J. [0000-0002-4480-1147]
- Subjects
Repressor Proteins ,Adolescent ,Brain Neoplasms ,Tumor Suppressor Proteins ,SCIENTIFIC CORRESPONDENCE ,Kruppel-Like Transcription Factors ,Trans-Activators ,Humans ,Female ,Gene Fusion ,Microtubule-Associated Proteins ,Neoplasms, Neuroepithelial ,health care economics and organizations - Abstract
Funder: Great Ormond Street Children’s Charity, Funder: The Brain Tumour Charity; Id: http://dx.doi.org/10.13039/501100002203, Funder: National Institute for Health Research; Id: http://dx.doi.org/10.13039/501100000272, Funder: Olivia Hodson Cancer Fund, Funder: CHILDREN with CANCER UK; Id: http://dx.doi.org/10.13039/501100001273, Funder: Cancer Research UK; Id: http://dx.doi.org/10.13039/501100000289, Funder: Wellcome Trust; Id: http://dx.doi.org/10.13039/100010269, Funder: Medical Research Council; Id: http://dx.doi.org/10.13039/501100000265
- Published
- 2021
3. Different Dimensions in Microbial Community Adaptation and Function
- Author
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Hitesh Tikariha and Hemant J. Purohit
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0106 biological sciences ,Functional role ,0303 health sciences ,030306 microbiology ,Computer science ,Functional redundancy ,Statistical model ,01 natural sciences ,Microbiology ,Data science ,03 medical and health sciences ,Conceptual framework ,010608 biotechnology ,Entropy (information theory) ,Scientific Correspondence - Abstract
With the omics tool, the challenges in understanding the microbial community functions are becoming more intriguing. It is the environment created scenario, which demands alignment of the different members of the community for the desired output leading to common condition for their survival. The resultant community pathways provide a broad umbrella of metabolic options giving the desired plasticity, which plays decision making role in the adaptation process. The initial step in community characterization must involve the discovery of key and core member of the community and monitoring the fluctuations in functional abundance over the space and time. The concept of entropy and metabolic fluxes must reflect the inner metabolic machinery of the taxon selection and route of functional operation in a community. The segregation of member based on their functional role and hierarchical level in the community must be an essential step to be followed by interaction mapping and measurement of metabolic fluxes to derive the flow of metabolites within the community. This conceptual framework and integrated omics tools with supported statistical modeling algorithm can help in bringing out finer details in the process of community functional adaptation in any given scenario.
- Published
- 2019
4. Response to comment on 'Lack of evidence for associative learning in pea plants'
- Author
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Kasey Markel
- Subjects
0301 basic medicine ,Plant growth ,replication ,QH301-705.5 ,Science ,Conditioning, Classical ,phototropism ,Plant Biology ,associative learning ,General Biochemistry, Genetics and Molecular Biology ,memory ,03 medical and health sciences ,0302 clinical medicine ,Replication (statistics) ,Biology (General) ,pisum sativum ,Cognitive science ,General Immunology and Microbiology ,Ecology ,General Neuroscience ,Peas ,General Medicine ,plant growth ,Plant biology ,Associative learning ,030104 developmental biology ,Medicine ,Other ,Psychology ,030217 neurology & neurosurgery ,Scientific Correspondence - Abstract
In 2016 Gagliano et al. reported evidence for associative learning in plants (Gagliano et al., 2016). A subsequent attempt to replicate this finding by the present author was not successful (Markel, 2020). Gagliano et al. attribute this lack of replication to differences in the experimental set-ups used in the original work and the replication attempt (Gagliano et al., 2020). Here, based on a comparison of the two set-ups, I argue that these differences are unable to explain the lack of replication in Markel, 2020.
- Published
- 2020
5. Impact of COVID-19 on Indian Sugar Industry
- Author
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M. Swapna, S. Solomon, and Govind Pratap Rao
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0106 biological sciences ,Coronavirus disease 2019 (COVID-19) ,media_common.quotation_subject ,Diversification (marketing strategy) ,01 natural sciences ,Agricultural economics ,National economy ,Spillover effect ,Sugar consumption ,Sugar ,Sugar price ,media_common ,Impact of corona ,business.industry ,Sugar industry ,Sugar export ,04 agricultural and veterinary sciences ,Agriculture ,Unemployment ,Diversification ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,business ,Agronomy and Crop Science ,human activities ,Scientific Correspondence ,010606 plant biology & botany - Abstract
The Indian sugar industry, a significant player in the national economy, has faced many challenges in the course of its journey. The threat posed by the growing pandemic novel corona virus (COVID-19), has been the most recent one and it is impacting sugar industry stakeholders and its integrated industries, not only in India, but all over the world. The entire value chain of the Indian sugar industry, viz., sugarcane, sugar, molasses, ethanol and their subsequent marketing and export, has been adversely affected from the spillover impacts. The major impacts of COVID-19 on Indian sugar industry are discussed.
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- 2020
6. Does ALS‐FUS without FUS mutation represent ALS‐FET? Report of three cases
- Author
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Borrego-Écija, S., Cortés-Vicente, E., Cervera-Carles, L., Clarimón, J., Gámez, J., Batlle, J., Ricken, Gerda, Molina-Porcel, L., Aldecoa, I., Sánchez-Valle, R., Rojas-García, R., Gelpi, E., Universitat Autònoma de Barcelona, Fundació La Marató de TV3, and European Commission
- Subjects
Male ,0301 basic medicine ,Histology ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,Physiology (medical) ,Humans ,Medicine ,Genetic Predisposition to Disease ,Age of Onset ,Aged ,business.industry ,Amyotrophic Lateral Sclerosis ,Middle Aged ,Molecular biology ,030104 developmental biology ,Neurology ,Mutation ,Mutation (genetic algorithm) ,RNA-Binding Protein FUS ,Female ,Neurology (clinical) ,Age of onset ,business ,Scientific Correspondence ,030217 neurology & neurosurgery - Abstract
Abnormal cytoplasmic accumulation of fused in sarcoma (FUS) protein is the pathological hallmark of some cases of amyotrophic lateral sclerosis (ALS) with transactive response DNA‐binding protein of 43KDa (TDP‐43)‐negative pathology that lack SOD1 mutations. FUS is an RNA‐binding protein located predominantly in the nucleus and is involved in regulation of transcription, alternative splicing, RNA stability, microRNA biogenesis, apoptosis and cell division. FUS, Ewing's sarcoma (EWS) and TATA‐binding protein‐associated factor 15 (TAF15) proteins constitute the FET (FUS/EWS/TAF15) family, highly conserved and ubiquitously expressed RNA‐binding proteins that shuttle between nucleus and cytoplasm assisted by the nuclear import protein Transportin 1 (Trn1), This study was partially funded by Fundació Marató de TV3 (grant no. 20143810 to RSV, no. 20141610 to EG and no. 201437.10 to RRG) and Fondo Europeo de Desarrollo Regional (FEDER) (PI16/01673 to JG and PI15/01618 to RRG).
- Published
- 2018
7. Methane as a Substrate for Energy Generation Using Microbial Fuel Cells
- Author
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Vipin Chandra Kalia, Jung-Kul Lee, Sanath Kondaveeti, and Gunda Mohanakrishna
- Subjects
0106 biological sciences ,0303 health sciences ,Bioelectrogenesis ,Microbial fuel cell ,biology ,030306 microbiology ,Chemistry ,business.industry ,Microbial consortium ,biology.organism_classification ,Combustion ,01 natural sciences ,Microbiology ,Methane ,03 medical and health sciences ,chemistry.chemical_compound ,Biogas ,Chemical engineering ,Natural gas ,010608 biotechnology ,business ,Scientific Correspondence ,Geobacter - Abstract
Methane (CH(4)) is a well-known and abundant feedstock for natural gas, and is readily available from various sources. In thermal plants, the CH(4) generated from anthropogenic sources is converted into electrical energy via combustion. Microbial fuel cell (MFC) technology has proven to be an efficient strategy for the biological conversion of a many substrates, including biogas (CH(4)), to electricity. MFC technology uses gaseous substrate along with an enriched and selective microbial consortium. Predominantly, methanotrophs and electrochemically active Geobacter were utilized in a syntrophic association on the anode of an MFC. This review focuses on the exploitation of CH(4) as a substrate for bioelectrogenesis via MFCs.
- Published
- 2018
8. Emerging Roles of Carotenoids in the Survival and Adaptations of Microbes
- Author
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Ramesh Kumar Saini, Iyyakkannu Sivanesan, and Young-Soo Keum
- Subjects
0106 biological sciences ,Cyanobacteria ,chemistry.chemical_classification ,0303 health sciences ,biology ,030306 microbiology ,organic chemicals ,food and beverages ,macromolecular substances ,biology.organism_classification ,Photosynthesis ,01 natural sciences ,Microbiology ,biological factors ,Sexual reproduction ,03 medical and health sciences ,chemistry ,010608 biotechnology ,Xanthophyll ,Botany ,polycyclic compounds ,Carotenoid ,Scientific Correspondence ,Xanthophyll Carotenoids - Abstract
Carotenoids belong to the widespread group of lipophilic tetraterpenoids that play essential roles in plants, microbes, and animals. In photosynthetic microalgae and cyanobacteria, carotenoids are the fundamental components of photosynthesis and protect these organisms from excess radiations, and oxidative stress. Also, polar xanthophyll carotenoids are well known to regulate the biophysical properties of cellular membranes with respect to corresponding changes in temperature. In Zygomycetes fungi, carotenoids-derived trisporoids play crucial roles in early sexual reproduction and mycelial development. Considering these multifaceted roles, carotenoids are widely researched on. In this article, we highlighted the emerging roles of carotenoids in the survival and adaptations of microalgae, bacteria, and fungi under normal as well as extreme environmental conditions.
- Published
- 2018
9. ABA Accumulation in Dehydrating Leaves Is Associated with Decline in Cell Volume, Not Turgor Pressure
- Author
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Lawren Sack, Thomas N. Buckley, and Grace P. John
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0106 biological sciences ,0301 basic medicine ,Physiology ,Plant Biology & Botany ,Turgor pressure ,Cell volume ,Plant Science ,Models, Biological ,01 natural sciences ,Cell size ,03 medical and health sciences ,Models ,Botany ,Pressure ,Genetics ,Cell Size ,Agricultural and Veterinary Sciences ,Dehydration ,Chemistry ,Abscisic acid metabolism ,Water ,Biological Sciences ,Biological ,Plant Leaves ,030104 developmental biology ,Volume (thermodynamics) ,Biophysics ,Water metabolism ,Scientific Correspondence ,Abscisic Acid ,010606 plant biology & botany - Abstract
Reanalysis of published experimental data shows that in dehydrating leaves ABA accumulation is linked with reduction of cell volume rather than turgor, providing clues toward signaling mechanisms.
- Published
- 2017
10. Response to comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'
- Author
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Christina Hertel, Anna Lorenc, Adrian Hayday, Annamari Ranki, Kai Kisand, Dmytro Fishman, Kai Krohn, Pärt Peterson, HUS Inflammation Center, and Department of Dermatology, Allergology and Venereology
- Subjects
0301 basic medicine ,immune tolerance ,type 1 diabetes ,T-Lymphocytes ,AUTOIMMUNITY ,Regulator ,CHILDREN ,Disease ,medicine.disease_cause ,Autoantigens ,Autoimmunity ,human B cell biology ,Immunology and Inflammation ,0302 clinical medicine ,False positive paradox ,Medicine ,Biology (General) ,Polyendocrinopathies, Autoimmune ,Human Biology & Physiology ,General Neuroscience ,General Medicine ,autoantigen ,autoantibodies and disease ,medicine.anatomical_structure ,Scientific Correspondence ,Human ,Model organisms ,INTERFERON ,QH301-705.5 ,Science ,T cell ,Immunology ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Humans ,APS1/APECED ,In patient ,Human Biology and Medicine ,Autoantibodies ,Type 1 diabetes ,General Immunology and Microbiology ,business.industry ,FOS: Clinical medicine ,Autoantibody ,medicine.disease ,030104 developmental biology ,13. Climate action ,3111 Biomedicine ,INHIBITORS ,business ,autoantibody ,Transcription Factors ,030215 immunology - Abstract
In 2016, we reported four substantial observations of APECED/APS1 patients, who are deficient in AIRE, a major regulator of central T cell tolerance (Meyer et al., 2016). Two of those observations have been challenged. Specifically, 'private' autoantibody reactivities shared by only a few patients but collectively targeting >1000 autoantigens have been attributed to false positives (Landegren, 2019). While acknowledging this risk, our study-design included follow-up validation, permitting us to adopt statistical approaches to also limit false negatives. Importantly, many such private specificities have now been validated by multiple, independent means including the autoantibodies ' molecular cloning and expression. Second, a significant correlation of antibody-mediated IFN a neutralization with an absence of disease in patients highly disposed to Type I diabetes has been challenged because of a claimed failure to replicate our findings (Landegren, 2019). However, flaws in design and implementation invalidate this challenge. Thus, our results present robust, insightful, independently validated depictions of APECED/APS1, that have spawned productive follow-up studies. Non
- Published
- 2019
11. Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
- Author
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Martin Karplus, Florent Hédin, Markus Meuwly, Krystel El Hage, and Prashant Kumar Gupta
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0301 basic medicine ,QH301-705.5 ,Science ,Structural Biology and Molecular Biophysics ,Systems biology ,box size ,Molecular Dynamics Simulation ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Hemoglobins ,thermodynamics ,03 medical and health sciences ,Molecular dynamics ,None ,0103 physical sciences ,Humans ,Statistical physics ,Biology (General) ,Protein Structure, Quaternary ,Physics ,Quantitative Biology::Biomolecules ,010304 chemical physics ,General Immunology and Microbiology ,Protein Stability ,General Neuroscience ,Molecular biophysics ,General Medicine ,hemoglobin ,molecular dynamics ,030104 developmental biology ,Structural biology ,kinetics ,Solvents ,Medicine ,Protein Multimerization ,Hydrophobic and Hydrophilic Interactions ,hydrophobic effect ,Scientific Correspondence ,Computational and Systems Biology ,Human - Abstract
Recent molecular dynamics (MD) simulations of human hemoglobin (Hb) give results in disagreement with experiment. Although it is known that the unliganded (T[Formula: see text]) and liganded (R[Formula: see text]) tetramers are stable in solution, the published MD simulations of T[Formula: see text] undergo a rapid quaternary transition to an R-like structure. We show that T[Formula: see text] is stable only when the periodic solvent box contains ten times more water molecules than the standard size for such simulations. The results suggest that such a large box is required for the hydrophobic effect, which stabilizes the T[Formula: see text] tetramer, to be manifested. Even in the largest box, T[Formula: see text] is not stable unless His146 is protonated, providing an atomistic validation of the Perutz model. The possibility that extra large boxes are required to obtain meaningful results will have to be considered in evaluating existing and future simulations of a wide range of systems.
- Published
- 2019
12. Response to comment on 'The distribution of antibiotic use and its association with antibiotic resistance'
- Author
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Scott W. Olesen, Yonatan H. Grad, and Marc Lipsitch
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0301 basic medicine ,medicine.medical_specialty ,antibiotic resistance ,QH301-705.5 ,Science ,education ,General Biochemistry, Genetics and Molecular Biology ,Antibiotic prescribing ,antibiotic use ,antibiotic prescribing ,03 medical and health sciences ,0302 clinical medicine ,Antibiotic resistance ,Internal medicine ,Medicine ,Biology (General) ,Antibiotic use ,reverse causality ,bacteria ,Reverse causality ,Microbiology and Infectious Disease ,General Immunology and Microbiology ,S. pyogenes ,business.industry ,General Neuroscience ,E. coli ,Drug Resistance, Microbial ,General Medicine ,humanities ,Anti-Bacterial Agents ,030104 developmental biology ,Epidemiology and Global Health ,antimicrobial ,epidemiology ,business ,030217 neurology & neurosurgery ,Scientific Correspondence - Abstract
We are writing to reply to the comment by Pouwels et al., 2019 about our recent study (Olesen et al., 2018) on antibiotic use and antibiotic resistance.
- Published
- 2019
13. Inositol Polyphosphate Binding Specificity of the Jasmonate Receptor Complex
- Author
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Sven T. Bitters, Nargis Parvin, Marek Dynowski, Haibin Mao, Debabrata Laha, Ning Zheng, Philipp Johnen, and Gabriel Schaaf
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Models, Molecular ,0106 biological sciences ,0301 basic medicine ,Receptor complex ,Physiology ,Arabidopsis ,Cyclopentanes ,Plant Science ,Plasma protein binding ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Polyphosphates ,Genetics ,Inositol ,Oxylipins ,Jasmonate ,Receptor ,Binding selectivity ,biology ,Arabidopsis Proteins ,Polyphosphate ,biology.organism_classification ,030104 developmental biology ,Biochemistry ,chemistry ,Scientific Correspondence ,Protein Binding ,010606 plant biology & botany - Abstract
Inositol polyphosphate binding specificity of the jasmonate receptor is largely determined by the F-box protein COI1.
- Published
- 2016
14. Comment on 'Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management'
- Author
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Danny Vereecke
- Subjects
0106 biological sciences ,0301 basic medicine ,QH301-705.5 ,Science ,Plant Biology ,Rhodococcus fascians ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Biology (General) ,leafy gall syndrome ,General Immunology and Microbiology ,biology ,General Neuroscience ,Rhodococcus corynebacterioides ,Environmental ethics ,General Medicine ,Biological evolution ,pistachio bushy top syndrome ,biology.organism_classification ,Plant biology ,Evolutionary transitions ,Plant development ,030104 developmental biology ,Medicine ,Other ,Rhodococcus ,Scientific Correspondence ,010606 plant biology & botany - Abstract
I would like to report significant issues of concern regarding this paper (Savory et al., 2017).
- Published
- 2018
15. Response to comment on 'Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans'
- Author
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Ben Clites, Bridgitte E. Palacios, Andrés G. Vidal-Gadea, Chance Bainbridge, Layla Bakhtiari, Vernita Gordon, and Jonathan T. Pierce-Shimomura
- Subjects
0301 basic medicine ,Nematode caenorhabditis elegans ,QH301-705.5 ,Science ,Model system ,Biology ,orientation ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Magnetotaxis ,Animals ,magnetosensation ,Biology (General) ,Caenorhabditis elegans ,Orientation, Spatial ,Neurons ,General Immunology and Microbiology ,behavior ,General Neuroscience ,Magnetoreception ,General Medicine ,biology.organism_classification ,Magnetic Fields ,030104 developmental biology ,Orientation (spatial) ,Earth's magnetic field ,C. elegans ,Medicine ,Experimental methods ,Neuroscience ,Scientific Correspondence - Abstract
Many animals can orient using the earth’s magnetic field. In a recent study, we performed three distinct behavioral assays providing evidence that the nematode Caenorhabditis elegans orients to earth-strength magnetic fields (Vidal-Gadea et al., 2015). A new study by Landler et al. suggests that C. elegans does not orient to magnetic fields (Landler et al., 2018). They also raise conceptual issues that cast doubt on our study. Here, we explain how they appear to have missed positive results in part by omitting controls and running assays longer than prescribed, so that worms switched their preferred migratory direction within single tests. We also highlight differences in experimental methods and interpretations that may explain our different results and conclusions. Together, these findings provide guidance on how to achieve robust magnetotaxis and reinforce our original finding that C. elegans is a suitable model system to study magnetoreception.
- Published
- 2018
16. Effect of Encapsulation on Viability of
- Author
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Ankita, Kataria, Sajan C, Achi, and Prakash M, Halami
- Subjects
Scientific Correspondence - Abstract
The health beneficial attributes of bifidobacteria and its safe association with the host gut has increased its significance as a probiotic. However delivering probiotic bifidobacteria with Minimum Biological Value (MBV) through product has always been a challenge. In the present study, an attempt was made to maintain the viability of native isolate of Bifidobacterium longum CFR 815j and deliver through ice-cream. B. longum CFR815j was microencapsulated in alginate starch capsules by emulsification followed by evaluation of bead stability in simulated gastrointestinal conditions. After incorporation in ice-cream, the effect on chemical properties, sensory parameters and meltdown characteristics of the product were also evaluated. Survival studies of B. longum revealed higher counts than 10(7) in the product which is essential for probiotic bacteria to exhibit beneficial effect. Further, all the properties of this ice-cream were comparable to the regular ice-cream. Our studies conclude that encapsulation was able to maintain the requisite MBV of bifidobacteria in ice-cream without affecting the sensory characteristics. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12088-018-0720-6) contains supplementary material, which is available to authorized users.
- Published
- 2017
17. On the Extent of Tyrosine Phosphorylation in Chloroplasts
- Author
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Qintao Lu, Stefan Helm, Anja Rödiger, and Sacha Baginsky
- Subjects
inorganic chemicals ,Proteomics ,Chloroplasts ,Physiology ,Molecular Sequence Data ,macromolecular substances ,Plant Science ,environment and public health ,chemistry.chemical_compound ,Arabidopsis ,Genetics ,Arabidopsis thaliana ,Amino Acid Sequence ,Phosphorylation ,Tyrosine ,Plant Proteins ,biology ,Kinase ,fungi ,Phosphoproteomics ,food and beverages ,Tyrosine phosphorylation ,Phosphoproteins ,biology.organism_classification ,Chloroplast ,enzymes and coenzymes (carbohydrates) ,chemistry ,Biochemistry ,bacteria ,Software ,Scientific Correspondence - Abstract
Tyr phosphorylation is a controversial issue in plant phosphoproteomics, ever since early analyses reported up to 5% Tyr phosphorylation in Arabidopsis ( Arabidopsis thaliana ), despite the lack of a classical Tyr kinase in the Arabidopsis genome ([Sugiyama et al., 2008][1]; [de la Fuente van Bentem
- Published
- 2015
18. Low Sugar Is Not Always Good: Impact of Specific O-Glycan Defects on Tip Growth in Arabidopsis
- Author
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J. Paul Knox, Silvina Mangano, Juan D. Salgado Salter, Eliana Marzol, Laercio Pol-Fachin, Hugo Verli, Norberto D. Iusem, Susan E. Marcus, José M. Estevez, Cecilia Borassi, Silvia Melina Velásquez, Martiniano M. Ricardi, Silvina Paola Denita Juárez, José R. Dinneny, and Javier Gloazzo Dorosz
- Subjects
Glycosylation ,animal structures ,Protein Conformation ,Physiology ,Meristem ,Mutant ,Arabidopsis ,macromolecular substances ,Plant Science ,Root hair ,Polysaccharides ,Genetics ,Tip growth ,O glycan ,Sugar ,Extensin ,Glycoproteins ,Plant Proteins ,biology ,Arabidopsis Proteins ,biology.organism_classification ,carbohydrates (lipids) ,Metabolic pathway ,Biochemistry ,biology.protein ,Biophysics ,lipids (amino acids, peptides, and proteins) ,Scientific Correspondence - Abstract
Mutants of the O-glycosylation pathway of extensins as well as molecular dynamics simulations uncover the effects of the O-glycosylation machinery on root hair tip growth.
- Published
- 2015
19. Targeted Mutagenesis of the Tomato PROCERA Gene Using Transcription Activator-Like Effector Nucleases
- Author
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David Weiss, Vai S. Lor, Daniel F. Voytas, Colby G. Starker, and Neil E. Olszewski
- Subjects
Crops, Agricultural ,Transcription activator-like effector nuclease ,Base Sequence ,Physiology ,Effector ,Molecular Sequence Data ,fungi ,Mutant ,food and beverages ,Plant Science ,Biology ,Endonucleases ,Cell biology ,Solanum lycopersicum ,Mutagenesis ,Transcription (biology) ,Botany ,Genetics ,Base sequence ,Gene ,Scientific Correspondence ,Plant Proteins - Abstract
Transcription activator-like effector nucleases successfully generate a heritable tomato mutant.
- Published
- 2014
20. Differential Accumulation of ELONGATED HYPOCOTYL5 Correlates with Hypocotyl Bending to Ultraviolet-B Light
- Author
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Filip Vandenbussche and Dominique Van Der Straeten
- Subjects
Arabidopsis Proteins ,Chromosomal Proteins, Non-Histone ,Ultraviolet Rays ,Physiology ,Gravitropism ,Arabidopsis ,Nuclear Proteins ,Ultraviolet b ,Plant Science ,Bending ,Biology ,Growth hormone ,Hypocotyl ,Basic-Leucine Zipper Transcription Factors ,Botany ,Genetics ,Biophysics ,Biological evidence ,Phototropism ,Scientific Correspondence ,Blue light - Abstract
To date, the main long-standing model explaining phototropic bending is that of [Cholodny (1927)][1] and [Went (1926)][2], which suggests that the lateral distribution of a growth hormone regulates phototropism and which is supported by a substantial amount of molecular and cell biological evidence
- Published
- 2014
21. Beyond the Theoretical Yields of Dark-Fermentative Biohydrogen
- Author
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Jung-Kul Lee, Sanjay K.S. Patel, and Vipin Chandra Kalia
- Subjects
0106 biological sciences ,Hydrogen ,Chemistry ,020209 energy ,Inorganic chemistry ,chemistry.chemical_element ,02 engineering and technology ,Dark fermentation ,01 natural sciences ,Microbiology ,010608 biotechnology ,Yield (chemistry) ,0202 electrical engineering, electronic engineering, information engineering ,Biohydrogen ,Sugar ,Scientific Correspondence - Abstract
Theoretical hydrogen (H(2)) yield by dark fermentative route is 12 mol/mol of glucose. Biological H(2) production yields of 3.8 mol/mol of glucose by microbes have been reported. Transient gene inactivation in combination with adaptive laboratory evolution strategy has enabled the H(2) yield to exceed the stoichiometric production values.
- Published
- 2018
22. A clinicopathological and genetic study of sporadic diffuse leukoencephalopathy with spheroids: a report of two cases
- Author
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Atsushi Sasaki, Kunihiro Yoshida, Nobuo Araki, Yoshihiko Nakazato, T. Kimura, Keisuke Ishizawa, Takashi Mitsufuji, and T. Abe
- Subjects
Pathology ,medicine.medical_specialty ,Histology ,TREM2 ,Biology ,medicine.disease ,Pathology and Forensic Medicine ,Leukoencephalopathy ,White matter ,Colony stimulating factor 1 receptor ,Myelin ,Exon ,medicine.anatomical_structure ,Neurology ,Physiology (medical) ,medicine ,Neurology (clinical) ,Gene ,Tyrosine kinase ,Scientific Correspondence - Abstract
Diffuse leukoencephalopathy with spheroids (DLS) is a white matter neurodegenerative disease characterized by progressive cognitive decline and motor symptoms 1–6, and histologically, by axonal swellings (‘spheroids’) and loss of axons and myelin 1–3,5,7–11. It was originally described as a rare, hereditary, autosomal dominant disorder (hereditary DLS: HDLS) 2, but there have been reports on DLS without family history as well (sporadic DLS: SDLS) 6,12–22. In 2012, Rademakers et al. 9 identified 14 different mutations in the colony stimulating factor 1 receptor (CSF1R) gene, which are located in exons 12–22 and affect the tyrosine kinase domain of the protein, in 14 families with HDLS. Interestingly, this gene shares the same signalling pathway as TYROBP (DAP12) and TREM2, whose mutations are implicated in polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy (PLOSL, also known as Nasu-Hakola disease) 23–25. PLOSL shares similar clinicopathological profiles with DLS, such as a progressive neuropsychiatric decline and leukoencephalopathy with spheroids 26,27. In this paper we describe the clinicopathological features of two cases of SDLS. In one of them, genetic analyses of CSF1R, TYROBP and TREM2 were conducted, and no mutations in these genes were identified.
- Published
- 2013
23. Free of acrylamide sodium dodecyl sulphate (SDS)-based tissue clearing (FASTClear): a novel protocol of tissue clearing for three-dimensional visualization of human brain tissues
- Author
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A K L, Liu, H M, Lai, R C-C, Chang, and S M, Gentleman
- Subjects
Imaging, Three-Dimensional ,Tissue Fixation ,Brain ,Humans ,Immunohistochemistry ,Scientific Correspondence - Published
- 2016
24. Discovery of New Modules in Metabolic Biology Using ChemoMetabolomics
- Author
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Natasha V. Raikhel, Asaph Aharoni, Lothar Willmitzer, and Samuel Bocobza
- Subjects
Protein function ,Physiology ,Chemistry, Organic ,Gene redundancy ,Metabolic network ,Genomics ,Plant Science ,Computational biology ,Biology ,Small molecule ,Mass Spectrometry ,Cell biology ,Metabolic pathway ,Crosstalk (biology) ,Metabolomics ,Genetics ,Metabolic Networks and Pathways ,Scientific Correspondence - Abstract
The use of small molecules to transiently modulate protein function can circumvent the limitations of classical genetic approaches caused by gene redundancy and lethality. Although chemical genomics and genetics screens facilitate the characterization of new biological components, they have infrequently led to the identification of target proteins involved in metabolism. The current state of metabolomics technologies permits the detection of thousands of molecules, allowing the exploration of yet uncharacterized metabolic pathways. The combination of these two approaches, termed here “ChemoMetabolomics”, is a promising application of both technologies. This novel approach will facilitate the detection of metabolic modulators, the dissection of the crosstalk in the metabolic network, and the development of hypotheses on how changes in metabolism affect developmental or cellular responses. Furthermore, it will facilitate the elucidation of the linkage between metabolic and developmental programs and assist the gain of an elaborated view of biological processes at the system level.
- Published
- 2012
25. Progress in Microbial Carotenoids Production
- Author
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Young-Soo Keum and Ramesh Kumar Saini
- Subjects
0106 biological sciences ,0301 basic medicine ,Antioxidant ,medicine.medical_treatment ,macromolecular substances ,Biology ,01 natural sciences ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Nutraceutical ,Astaxanthin ,010608 biotechnology ,polycyclic compounds ,medicine ,Carotenoid ,chemistry.chemical_classification ,business.industry ,organic chemicals ,food and beverages ,Environmentally friendly ,biological factors ,Biotechnology ,030104 developmental biology ,chemistry ,business ,Scientific Correspondence - Abstract
Carotenoids are versatile isoprenoids pigments, play a vital role in the cellular system, starting from antioxidant to gene regulation. Carotenoids are widely used in food, nutraceuticals, and cosmetics owing to their vitamin A, antioxidant and anticancer activities. The demand of carotenoids in various sectors has triggered the research to explore a commercially viable and environmentally friendly production. This article presents a short review of progress in carotenoids production from microbial platforms.
- Published
- 2017
26. Are Natural Deep Eutectic Solvents the Missing Link in Understanding Cellular Metabolism and Physiology?
- Author
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Jaap van Spronsen, Frank Hollmann, Geert-Jan Witkamp, Young Hae Choi, Robert Verpoorte, Yuntao Dai, Isabel W. C. E. Arends, and Marianne C. Verberne
- Subjects
Cellular metabolism ,010405 organic chemistry ,Physiology ,Rutin ,Laccase ,Ionic Liquids ,02 engineering and technology ,Plant Science ,Biology ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Metabolomics ,Solubility ,Plant Cells ,Solvents ,Genetics ,Cleome ,0210 nano-technology ,Nuclear Magnetic Resonance, Biomolecular ,Scientific Correspondence - Abstract
Over the past decade, metabolomics has developed into a major tool for studying the metabolism of organisms and cells, and through this approach much has been learned about metabolic networks and the reactions of organisms to various external conditions ([Lay et al., 2006][1]). Most of this work
- Published
- 2011
27. The Role of Brassinosteroids in Shoot Gravitropism
- Author
-
Liesbeth De Grauwe, Kris Vissenberg, Dominique Van Der Straeten, Filip Vandenbussche, Olivier Leroux, and Dmitry Suslov
- Subjects
Sucrose ,Physiology ,Starch ,Gravitropism ,Arabidopsis ,Plant Science ,Hypocotyl ,chemistry.chemical_compound ,Steroids, Heterocyclic ,Cell Wall ,Auxin ,Brassinosteroids ,Botany ,Genetics ,Arabidopsis thaliana ,Amyloplast ,Biology ,chemistry.chemical_classification ,integumentary system ,biology ,fungi ,food and beverages ,biology.organism_classification ,chemistry ,Seedlings ,Shoot ,Endodermis ,Cholestanols ,Plant Shoots ,Scientific Correspondence - Abstract
In the current model of gravitropism, negative gravitropic (upward) growth of the shoot of a dicotyledonous plant involves sedimentation of starch-containing plastids (statoliths) in the endodermis (starch sheath). Here we show that high levels of brassinosteroids (BRs) counteract gravitropic growth, while BR deficiency enhances gravitropism irrespective of the presence of a functional starch sheath. These data support a role for BRs as negative regulators of the shoot graviresponse.
- Published
- 2011
28. Interconnection between Methyl Salicylate and Lipid-Based Long-Distance Signaling during the Development of Systemic Acquired Resistance in Arabidopsis and Tobacco
- Author
-
Sang-Wook Park, Po-Pu Liu, Caroline C. von Dahl, and Daniel F. Klessig
- Subjects
Physiology ,Molecular Sequence Data ,Arabidopsis ,Plant Science ,Biology ,Fatty Acid-Binding Proteins ,Microbiology ,Broad spectrum ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Tobacco ,Genetics ,Regulation of gene expression ,Arabidopsis Proteins ,fungi ,Methyltransferases ,biology.organism_classification ,Lipids ,Immunity, Innate ,Salicylates ,chemistry ,Biochemistry ,Mutation ,Signal transduction ,Carrier Proteins ,Scientific Correspondence ,Systemic acquired resistance ,Salicylic acid ,Methyl salicylate ,Signal Transduction - Abstract
Systemic acquired resistance (SAR) is a salicylic acid (SA)-dependent heightened state of resistance against a broad spectrum of pathogens activated in the uninoculated systemic tissue of a pathogen-infected plant. For systemic protection to be initiated, a mobile signal that is produced at the site
- Published
- 2011
29. Draft Genome Sequences of Yersinia pestis Strains from the 1994 Plague Epidemic of Surat and 2002 Shimla Outbreak in India
- Author
-
Dhiraj P. Dhotre, Pradyumna S. Paranjape, Nachiket P. Marathe, Sudarshan A. Shetty, Avinash Sharma, Urmil Tuteja, Yogesh S. Shouche, Harsh Vardhan Batra, Somak Chowdhury, Kiran N. Mahale, and Kaushal Sharma
- Subjects
Yersinia pestis ,biology ,Contig ,Strain (biology) ,Outbreak ,biology.organism_classification ,Plague (disease) ,Microbiology ,Genome size ,Virology ,Genome ,Scientific Correspondence ,Deep sequencing - Abstract
We report the first draft genome sequences of the strains of plague-causing bacteria, Yersinia pestis, from India. These include two strains from the Surat epidemic (1994), one strain from the Shimla outbreak (2002) and one strain from the plague surveillance activity in the Deccan plateau region (1998). Genome size for all four strains is ~4.49 million bp with 139–147 contigs. Average sequencing depth for all four genomes was 21x.
- Published
- 2014
30. Candidate OP Phyla: Importance, Ecology and Cultivation Prospects
- Author
-
M. Rohini Kumar and Venkatakrishnan Sivaraj Saravanan
- Subjects
Bioprospecting ,Phylum ,Ecology ,Ecology (disciplines) ,genetic processes ,information science ,Ribosomal RNA ,Biology ,16S ribosomal RNA ,Microbiology ,DNA sequencing ,Microbial ecology ,bacteria ,Scientific Correspondence - Abstract
OP phyla were created in the domain bacteria, based on the group of 16S rRNA gene sequences recovered from the Obsidian Pool. However, due to the lack of cultured representative it is referred to as candidate phyla. Wider ecological occurrence was predicted for the OP phyla, especially OP3, OP10 and OP11. Recently, members of phylum OP5 and OP10 were cultured, providing clues to their cultivation prospects. At last the bioprospecting potentials of the OP members are discussed herein.
- Published
- 2010
31. Reevaluation of Abscisic Acid-Binding Assays Shows That G-Protein-Coupled Receptor2 Does Not Bind Abscisic Acid
- Author
-
Joanna M. Risk, Catherine L. Day, and Richard C. Macknight
- Subjects
Arabidopsis Proteins ,Physiology ,G protein ,Recombinant Fusion Proteins ,Arabidopsis ,RNA-Binding Proteins ,Reproducibility of Results ,Plant physiology ,Receptors, CCR10 ,Plant Science ,Biology ,DNA-binding protein ,Abscisic acid binding ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Escherichia coli ,Genetics ,Binding site ,Signal transduction ,Receptor ,Abscisic acid ,Scientific Correspondence ,Abscisic Acid - Abstract
The phytohormone abscisic acid (ABA) plays an integral role in plant growth and development, but only recently have putative receptors been identified ([Razem et al., 2006][1]; [Shen et al., 2006][2]; [Liu et al., 2007][3]; [Pandey et al., 2009][4]). Our results, however, suggest that the putative
- Published
- 2009
32. Activity Range of Arabidopsis Small RNAs Derived from Different Biogenesis Pathways
- Author
-
Yuval Eshed, Elsa M. Tretter, John Paul Alvarez, and John L. Bowman
- Subjects
Genetics ,RNA, Untranslated ,Physiology ,Trans-acting siRNA ,Arabidopsis ,RNA ,Plant Science ,Argonaute ,Biology ,Non-coding RNA ,Long non-coding RNA ,Biosynthetic Pathways ,Cell biology ,MicroRNAs ,RNA silencing ,Gene Expression Regulation, Plant ,RNA, Plant ,DNA-directed RNA interference ,RNA, Small Interfering ,Small nucleolar RNA ,Scientific Correspondence - Abstract
Several classes of small RNAs are known in plants and accumulating evidence indicates that different classes of small RNAs may function either cell autonomously or noncell autonomously to regulate gene expression. Here, a simple visual assay used to compare the biological activity of small RNAs
- Published
- 2008
33. Tryptophan-Independent Indole-3-Acetic Acid Synthesis: Critical Evaluation of the Evidence
- Author
-
Heather M. Nonhebel
- Subjects
Physiology ,Stereochemistry ,Arabidopsis ,Tryptophan synthase ,Plant Science ,Zea mays ,chemistry.chemical_compound ,Solanum lycopersicum ,Botany ,Genetics ,Tryptophan Synthase ,Arabidopsis thaliana ,heterocyclic compounds ,Phylogeny ,Plant Proteins ,biology ,Indoleacetic Acids ,Tryptophan ,food and beverages ,respiratory system ,Plants ,biology.organism_classification ,humanities ,chemistry ,Mutation ,biology.protein ,Indole-3-acetic acid ,Scientific Correspondence - Abstract
Trp-independent synthesis of indole-3-acetic acid ([IAA][1]) was proposed back in the early 1990s based on observations from Trp auxotrophs in maize ( Zea mays ; [Wright et al., 1991][2]) and Arabidopsis ( Arabidopsis thaliana ; [Normanly et al., 1993][3]). Recently, [Wang et al. (2015)][4]
- Published
- 2015
34. General and Analytic Solutions of the Ortega Equation
- Author
-
Sylwia Lewicka
- Subjects
Physics ,Physiology ,Differential equation ,Mathematical analysis ,Plant Development ,Water ,Plant Science ,Extension (predicate logic) ,Cell Enlargement ,Plants ,Models, Biological ,Cell Wall ,Simple (abstract algebra) ,Plant Cells ,Genetics ,Scientific Correspondence - Abstract
[Ortega (1985)][1] proposed a simple first-order differential equation to describe plant cell extension and, unlike the Lockhart equation ([Lockhart, 1965][2]), it takes into account elastic deformation of the cell wall. [Cosgrove (1985)][3] and [Ortega (1985)][1] solved the equation for the
- Published
- 2006
35. Overrepresentation of Elements Recognized by TCP-Domain Transcription Factors in the Upstream Regions of Nuclear Genes Encoding Components of the Mitochondrial Oxidative Phosphorylation Machinery
- Author
-
Elina Welchen and Daniel H. Gonzalez
- Subjects
Nuclear gene ,Physiology ,Plant Science ,Biology ,Mitochondrion ,Oxidative Phosphorylation ,Ciencias Biológicas ,Mitochondrial biogenesis ,Arabidopsis ,Genetics ,medicine ,Arabidopsis thaliana ,TCP domain ,Gene ,Transcription factor ,Cell Nucleus ,food and beverages ,Promoter ,Bioquímica y Biología Molecular ,biology.organism_classification ,Mitochondria ,Cell nucleus ,medicine.anatomical_structure ,Gene expression ,Scientific Correspondence ,CIENCIAS NATURALES Y EXACTAS ,Transcription Factors - Abstract
We have observed that a cis-acting regulatory element, known as site II, is overrepresented in the promoters of nuclear genes encoding components of the oxidative phosphorylation (OxPhos) machinery from both Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Site II elements have been described in promoters of rice and Arabidopsis proliferating cell nuclear antigen (PCNA) genes (Kosugi et al., 1995; Tre´mousaygue et al., 2003) and are also present in the majority of Arabidopsis genes encoding ribosomal proteins (Tre´mousaygue et al., 2003). Loss-of-function analysis has determined that a pair of site II elements present in the rice PCNA promoter is essential for the expression of a reporter gene in the shoot and root meristems of transgenic tobacco (Nicotiana tabacum; Kosugi et al., 1991, 1995). In fact, a promoter region containing these elements is enough to confer expression in tobacco protoplasts when fused to a minimal promoter (Kosugi et al., 1995). Similar elements in Arabidopsis PCNA-2 produce expression in root primordia and young leaves (Tre´mousaygue et al., 2003). Accordingly, these elements have been implicated in the expression of genes in meristematic tissues and/or proliferating cells. Site II elements are frequently present in more than one copy and found in combination with another motif, known as telo box or internal telomeric repeat due to its similarity to the repeated unit of plant telomeres (Tre´mousaygue et al., 2003) Fil: Welchen, Elina. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina Fil: Gonzalez, Daniel Hector. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas; Argentina
- Published
- 2006
36. Sequencing Multiple and Diverse Rice Varieties. Connecting Whole-Genome Variation with Phenotypes
- Author
-
Kenneth L. McNally, Jan E. Leach, C. Robin Buell, Hei Leung, Richard Bruskiewich, and David J. Mackill
- Subjects
Oryza sativa ,Physiology ,business.industry ,Plant genetics ,food and beverages ,Oryza ,Genomics ,Sequence Analysis, DNA ,Plant Science ,Biology ,Polymorphism, Single Nucleotide ,Phenotype ,Biotechnology ,Genome variation ,Research community ,Genetic variation ,Genetics ,business ,Functional genomics ,Scientific Correspondence ,Genome, Plant ,Phylogeny - Abstract
The International Rice Functional Genomics Consortium (IRFGC) has initiated a project to provide the rice research community with access to extensive information on genetic variation present within and between diverse rice cultivars and landraces, as well as the genetic resources to exploit that
- Published
- 2006
37. The Plant VirE2 Interacting Protein 1. A Molecular Link between the Agrobacterium T-Complex and the Host Cell Chromatin?
- Author
-
Stanislav V. Kozlovsky, Tzvi Tzfira, Nehama Zakai, Joseph Rosenbluh, Vitaly Citovsky, Abraham Loyter, and Jianxiong Li
- Subjects
Physiology ,Agrobacterium ,education ,Plant Science ,DNA-binding protein ,Ion Channels ,Histones ,chemistry.chemical_compound ,Bacterial Proteins ,Genetics ,biology ,fungi ,Membrane Proteins ,food and beverages ,Agrobacterium tumefaciens ,Plant cell ,biology.organism_classification ,Chromatin ,humanities ,DNA-Binding Proteins ,Kinetics ,Histone ,Membrane protein ,chemistry ,biology.protein ,bacteria ,Scientific Correspondence ,DNA - Abstract
The microbe Agrobacterium tumefaciens is harmful to plants and useful to scientists for one and the same reason: It transfers DNA into plant genomes. Found in soil worldwide, Agrobacterium causes disease in plants by transferring its own DNA into plant cells. But in the laboratory, the ability to
- Published
- 2005
38. Tools to Study Plant Organelle Biogenesis. Point Mutation Lines with Disrupted Vacuoles and High-Speed Confocal Screening of Green Fluorescent Protein-Tagged Organelles
- Author
-
Jan Zouhar, S. Narasimha Chary, David G. Carter, Emily L. Avila, Natasha V. Raikhel, and April E. Agee
- Subjects
Cell division ,Physiology ,Confocal ,Green Fluorescent Proteins ,Plant Science ,Vacuole ,Biology ,Green fluorescent protein ,Genes, Reporter ,Organelle ,Genetics ,Point Mutation ,Organelles ,Microscopy, Confocal ,Organelle Biogenesis ,fungi ,food and beverages ,Plants, Genetically Modified ,Plant cell ,Recombinant Proteins ,Cell biology ,Luminescent Proteins ,Vacuoles ,Organelle biogenesis ,Scientific Correspondence ,Biogenesis - Abstract
We have focused our studies in the past several years on understanding protein trafficking from the secretory system to the vacuole—an organelle present in all plant cells. Here, we report an approach for generating and screening plants with defects in vacuolar biogenesis. Plant vacuoles are
- Published
- 2003
39. Chemical Genetic Approaches to Plant Biology
- Author
-
Yunde Zhao and Helen E. Blackwell
- Subjects
Physiology ,Agrochemical ,business.industry ,Arabidopsis ,Plant Science ,Plants ,Biology ,Plant biology ,Plant Physiological Phenomena ,Organic molecules ,Biochemistry ,Genetics ,Biochemical engineering ,business ,Scientific Correspondence - Abstract
Synthetic chemistry and plant biology intersect in myriad ways. To date, however, the overlap of research methods between these two fields is limited. Outside of the agrochemical industry, most synthetic chemists simply view plants as sources of diverse and structurally complex organic molecules (i.
- Published
- 2003
40. Control of Ascorbate Synthesis by Respiration and Its Implications for Stress Responses
- Author
-
Frederica L. Theodoulou, Valentina Mittova, Christine H. Foyer, A. Harvey Millar, Joshua L. Heazlewood, Carlos Guillermo Bartoli, and Guy Kiddle
- Subjects
Oxidoreductases Acting on CH-CH Group Donors ,Physiology ,Molecular Sequence Data ,Arabidopsis ,Potassium cyanide ,Dehydrogenase ,Ascorbic Acid ,Plant Science ,Mitochondrion ,Biology ,chemistry.chemical_compound ,Oxygen Consumption ,Biosynthesis ,Oxidoreductase ,Rotenone ,Respiration ,Genetics ,Amino Acid Sequence ,Ciencias Agrarias ,Potassium Cyanide ,chemistry.chemical_classification ,fungi ,food and beverages ,Galactonolactone dehydrogenase ,Plants ,ascorbate ,Ascorbic acid ,Peptide Fragments ,Mitochondria ,Biochemistry ,chemistry ,Scientific Correspondence ,respiration - Abstract
We show for the first time that respiration can control ascorbate (AA) synthesis in plants. Evidence for this control is provided by (a) the localization of L-galactono-1,4-lactone dehydrogenase (GalLDH), the terminal enzyme in AA biosynthesis, with mitochondrial complex I, and its regulation by electron transport through this complex, (b) the absolute requirement of the enzyme for oxidized cytochrome c (cyt c(ox)) as substrate, and (c) the coordinated response of respiration and AA synthesis to stress induced by hormone treatment., Instituto de Fisiología Vegetal, Facultad de Ciencias Agrarias y Forestales
- Published
- 2003
41. Mitochondrial and Cytosolic Calcium Dynamics Are Differentially Regulated in Plants
- Author
-
Marc R. Knight and David C. Logan
- Subjects
Physiology ,Recombinant Fusion Proteins ,Green Fluorescent Proteins ,Arabidopsis ,Aequorin ,chemistry.chemical_element ,Plant Science ,Calcium ,Cytosol ,Gene Expression Regulation, Plant ,In vivo ,Genetics ,Mannitol ,Calcium Signaling ,biology ,Dynamics (mechanics) ,Hydrogen Peroxide ,Plant cell ,Mitochondria ,Cold Temperature ,Luminescent Proteins ,Proton-Translocating ATPases ,chemistry ,Biochemistry ,Free calcium ,biology.protein ,Scientific Correspondence ,Cytosolic calcium - Abstract
The role of mitochondrial calcium in plant cell signaling has received little attention due to the technical difficulties in measuring changes in the mitochondrial free calcium concentration ([Ca2+]m) in vivo. Here, we describe the unprecedented use of targeted aequorin to produce stably transformed
- Published
- 2003
42. Mycorrhizal Fungi Can Dominate Phosphate Supply to Plants Irrespective of Growth Responses
- Author
-
F. Andrew Smith, Sally E. Smith, and Iver Jakobsen
- Subjects
Physiology ,Plant Development ,Plant Science ,Biology ,Plant Roots ,Phosphates ,chemistry.chemical_compound ,Periarbuscular membrane ,Symbiosis ,Mycorrhizae ,Mycorrhizal fungi ,Botany ,Genetics ,Ecology ,Plant roots ,fungi ,food and beverages ,Agriculture ,Plants ,Phosphate ,chemistry ,Agronomy ,Mycotroph ,Terrestrial ecosystem ,Arbuscular mycorrhizal ,Scientific Correspondence - Abstract
Arbuscular mycorrhizal (AM) fungi are vital components of nearly all terrestrial ecosystems, forming mutually beneficial (mutualistic) symbioses with the roots of around 80% of vascular plants and often increasing phosphate (P) uptake and growth. We present novel data showing that AM fungi can
- Published
- 2003
43. Experimental Approach to Elucidating the Mechanism of Light-Independent Chlorophyll Biosynthesis in Greening Barley
- Author
-
Victor Raskin and Amnon Schwartz
- Subjects
Chlorophyll ,Oxidoreductases Acting on CH-CH Group Donors ,Chlorophyll a ,Light ,Physiology ,Plant Science ,Biology ,chemistry.chemical_compound ,Ascorbate Peroxidases ,Greening ,Protochlorophyllide ,Botany ,Genetics ,Carbon Radioisotopes ,Chlorophyllides ,Hydrogen peroxide metabolism ,Chlorophyll A ,Hordeum ,Hydrogen Peroxide ,Plant Leaves ,Peroxidases ,chemistry ,Etiolation ,Darkness ,Light-independent chlorophyll biosynthesis ,Hordeum vulgare ,Salicylic Acid ,Scientific Correspondence - Abstract
Etiolated seedlings of angiosperms illuminated for a few hours and then returned to darkness continue to accumulate chlorophyll (Chl) a ([Popov and Dilova, 1969][1]; [Adamson et al., 1997][2], and refs. therein). In leaves of barley ( Hordeum vulgare ) seedlings and leaves of Tradescancia albiflora
- Published
- 2003
44. Redox Control of Protein Tyrosine Phosphatases and Mitogen-Activated Protein Kinases in Plants
- Author
-
Sheng Luan and Rajeev Gupta
- Subjects
Soil salinity ,Physiology ,Arabidopsis ,Plant Science ,Protein tyrosine phosphatase ,medicine.disease_cause ,Redox ,Receptor tyrosine kinase ,Genetics ,medicine ,biology ,Chemistry ,Kinase ,food and beverages ,Hydrogen Peroxide ,Plant cell ,Cell biology ,Oxidative Stress ,Biochemistry ,Mitogen-activated protein kinase ,biology.protein ,Mitogen-Activated Protein Kinases ,Protein Tyrosine Phosphatases ,Oxidation-Reduction ,Scientific Correspondence ,Oxidative stress - Abstract
Environmental conditions, including light, temperature, water status, and soil salinity, all modify the redox state of plant cells ([Allen et al., 1995][1]). A number of studies have shown that oxidative stress is a common factor that affects plant growth and development under extreme environmental
- Published
- 2003
45. H626R and R124C mutations of the TGFBI (BIGH3) gene caused lattice corneal dystrophy in Vietnamese people
- Author
-
L X Cung, K Fujiki, A Kanai, N T Ha, T K Thanh, H M Chau, and Akira Murakami
- Subjects
Adult ,Male ,Vietnamese ,Biology ,law.invention ,Transforming Growth Factor beta1 ,Cellular and Molecular Neuroscience ,Transforming Growth Factor beta ,law ,Cornea ,medicine ,Humans ,Gene ,Polymerase chain reaction ,Aged ,Corneal Dystrophies, Hereditary ,Genetics ,Middle Aged ,medicine.disease ,Phenotype ,eye diseases ,Sensory Systems ,language.human_language ,Pedigree ,Ophthalmology ,genomic DNA ,medicine.anatomical_structure ,Vietnam ,Mutation ,language ,Lattice corneal dystrophy ,Female ,Scientific Correspondence ,TGFBI - Abstract
Background/aims: Mutations of the human transforming growth factor β induced gene (TGFBI) were reported to cause lattice corneal dystrophy (LCD) in various nationalities. This study analysed the TGFBI gene in Vietnamese people with LCD. Methods: 13 unrelated families, including 34 patients and 21 unaffected members were examined. 50 normal Vietnamese people served as controls. Blood samples were collected. Genomic DNA was extracted from leucocytes. Analysis of TGFBI gene was performed using the polymerase chain reaction and direct sequencing. Corneal buttons were studied histopathologically. Results: Two clinically distinguishable forms of LCD were revealed: one was typical of LCDI; the other was characterised by the late onset, thick lattice lines, and asymmetry between two eyes. Sequencing of the TGFBI gene revealed R124C mutation in three families and H626R mutation in 10 families. Congo red staining of the H626R-LCD cornea showed amyloid deposits in the subepithelial and stromal layers. Conclusions: R124C and H626R mutations of TGFBI gene caused LCD in Vietnamese people. R124C, a common cause of LCDI in many nationalities, was relatively rare, whereas H626R reported in several white people but not yet in Asians was most common (>75%) in Vietnamese people. Since the phenotype caused by H626R represents a new variant intermediate between LCDI and LCDIIIA, we proposed to consider it as LCD type IIIB.
- Published
- 2003
46. Comparison of localised nerve fibre layer defects in normal tension glaucoma and primary open angle glaucoma
- Author
-
Kyu Hyung Park, Se Joon Woo, and Dong Myung Kim
- Subjects
Adult ,Male ,Intraocular pressure ,medicine.medical_specialty ,genetic structures ,Open angle glaucoma ,Glaucoma ,Nerve fibre layer ,Cellular and Molecular Neuroscience ,chemistry.chemical_compound ,Nerve Fibers ,Ophthalmology ,Normal tension glaucoma ,Optic Nerve Diseases ,medicine ,Humans ,Statistical analysis ,Aged ,Retrospective Studies ,business.industry ,Retinal ,Middle Aged ,medicine.disease ,eye diseases ,Sensory Systems ,Low Tension Glaucoma ,chemistry ,Optometry ,Female ,sense organs ,business ,Scientific Correspondence - Abstract
To compare the pattern of localised nerve fibre layer (NFL) defects in normal tension glaucoma (NTG) and primary open angle glaucoma (POAG).50 NTG eyes and 36 POAG eyes, all with localised NFL defects, were enrolled. On retinal NFL photography, the proximity of the defect to the centre of the fovea (angle alpha) and the sum of the angular width of the defects (angle beta) were determined. Angle alpha was the angle made by a line from the centre of the fovea to the disc centre and a line from the disc centre to the disc margin, where the nearest border of the defect met. The patterns of localised NFL defects in NTG and POAG were compared with angles alpha and beta. Independent t test was used for statistical analysis.Angle alpha in NTG (35.1 (SD 20.0) degrees ) was significantly smaller than that of POAG (45.9 (21.9) degrees ) (p=0.02), while angle beta in NTG (49.0 (31.9) degrees ) was significantly larger than that of POAG (33.1 (23.9) degrees ) (p=0.01).The pattern of NFL defects in NTG was different from that in POAG. Localised NFL defects in NTG were closer to the fovea and wider in width than those in POAG.
- Published
- 2003
47. A comparison of perimetric results with the Medmont and Humphrey perimeters
- Author
-
Alok Sharma, Stuart L. Graham, Ivan Goldberg, and John A Landers
- Subjects
Male ,genetic structures ,Glaucoma ,Flicker fusion threshold ,behavioral disciplines and activities ,Flicker Fusion ,Perimeter ,Cellular and Molecular Neuroscience ,Cohen's kappa ,Sensory threshold ,mental disorders ,Humans ,Medicine ,Receiver operating characteristic ,business.industry ,Flicker ,Middle Aged ,medicine.disease ,eye diseases ,Sensory Systems ,Ophthalmology ,ROC Curve ,Area Under Curve ,Sensory Thresholds ,Visual Field Tests ,Optometry ,Female ,Visual field loss ,Visual Fields ,business ,Scientific Correspondence - Abstract
Background: The Humphrey field analyser (HFA), Humphrey-Zeiss frequency doubling perimeter, and the Medmont automated perimeter (MAP) are three commonly used automated perimeters with threshold achromatic methodologies. Visual field loss may be detected earlier with strategies that target cell lines with reduced redundancy or which suffer selective damage. Method: To compare these three perimeters, 63 subjects who were glaucoma suspects, ocular hypertensives, glaucoma patients, or normal controls were recruited selectively. All subjects underwent testing using MAP central threshold, MAP flicker perimetry, HFA full threshold, HFA SITA perimetry, HFA short wavelength perimetry (SWAP), and frequency doubling perimetry (FDP). After visual field testing, equivalent tests were compared: MAP central threshold with HFA full threshold and HFA SITA perimetry; Medmont flicker perimetry with HFA SWAP and FDP. Results: On analysis of the MAP central threshold a kappa statistic and an area under the receiver operator curve (AUC) of 0.90 and 0.94, respectively, were found compared with HFA full threshold strategies, and 0.87 and 0.92 respectively, compared with HFA SITA. For MAP flicker a kappa statistic and an AUC of 0.65 and 0.81, respectively, were found compared with HFA SWAP and 0.87 and 0.96, respectively, compared with FDP. A quadrant analysis and comparison of mean defect between tests was also highly significant. Conclusion: Medmont and Humphrey perimeters correlated well; both may be used for clinical and research purposes with similar confidence.
- Published
- 2003
48. Keratoplasty for keratomalacia in preschool children
- Author
-
Rasik B Vajpayee, J S Titiyal, M Vanathi, Namrata Sharma, and Radhika Tandon
- Subjects
Diarrhea ,Male ,Iridectomy ,medicine.medical_specialty ,Visual acuity ,genetic structures ,Eye disease ,Population ,Visual Acuity ,Measles ,Corneal Diseases ,Cornea ,Corneal Transplantation ,Cellular and Molecular Neuroscience ,Keratomalacia ,medicine ,Humans ,education ,education.field_of_study ,business.industry ,Infant ,Pneumonia ,medicine.disease ,Sensory Systems ,Surgery ,Ophthalmology ,Treatment Outcome ,El Niño ,Child, Preschool ,Acute Disease ,Female ,medicine.symptom ,business ,Keratoplasty, Penetrating ,Scientific Correspondence ,Ophthalmologic Surgical Procedure - Abstract
Aim: To study the results of surgical management of keratomalacia in children. Methods: A clinical case series of all children with keratomalacia, admitted to an Indian centre during the period from June 2000 to June 2001 is presented. The parameters evaluated were demographic data, systemic associations, and results of medical and surgical intervention. Results: 29 children with keratomalacia ranging from 2 months to 5 years of age (mean 1.8 (SD 1.4) years) were included in the study. All children belonged to families of lower socioeconomic status. 27 patients (93.1%) had not been immunised at all. The systemic diseases precipitating the onset of keratomalacia included measles (41.37%), pneumonia (31.03%), and acute diarrhoea (37.93%). 36 eyes (66.7%) had total corneal melting and 11 (20.3%) eyes had paracentral corneal melting. In 15 eyes (27.8%) an emergency tectonic penetrating keratoplasty was performed of which only five grafts (33.3%) remained clear at a mean follow up of 7.3 (6.8) months (range 3–24 months). Seven eyes underwent optical penetrating keratoplasty, of which four grafts (57.14%) remained clear at a mean follow up of 6.4 (3.6) months (range 3–12 months). None of these could achieve a visual acuity better than 6/60. Conclusions: Corneal grafting surgery in keratomalacia is associated with poor visual outcome.
- Published
- 2003
49. Rapid and Efficient Suppression of Gene Expression in a Single-Cell Model System, Ceratopteris richardii
- Author
-
Sarah Archer-Evans, Gregory B. Clark, Stephen C. Stout, and Stanley J. Roux
- Subjects
Expressed Sequence Tags ,Spores ,Genetics ,Regulation of gene expression ,Light ,biology ,Physiology ,Molecular Sequence Data ,Chatterjee ,Cell model ,Plant Science ,biology.organism_classification ,Molecular biology ,Gene Expression Regulation, Plant ,Culture Techniques ,Gene expression ,Ferns ,RNA-Induced Silencing Complex ,RNA Interference ,Ceratopteris richardii ,RNA, Small Interfering ,Scientific Correspondence ,Signal Transduction - Abstract
Germinating Ceratopteris richardii spores have proven to be a useful single-cell system for analyzing light and gravity regulation of development ([Cooke et al., 1995][1]; [Banks, 1999][2]; [Chatterjee and Roux, 2000][3]; [Murata and Sugai, 2000][4]), but the lack of a gene sequence database and of
- Published
- 2003
50. Effect of a patient training video on visual field test reliability
- Author
-
John M Sparrow, Paul G. D. Spry, Jeremy P. Diamond, A Waldock, and H Sherafat
- Subjects
Male ,medicine.medical_specialty ,Intraocular pressure ,Glaucoma ,Audiology ,law.invention ,Cellular and Molecular Neuroscience ,Patient Education as Topic ,Randomized controlled trial ,law ,Humans ,Medicine ,Prospective Studies ,Vision test ,Reliability (statistics) ,Aged ,medicine.diagnostic_test ,business.industry ,Vision Tests ,Reproducibility of Results ,Videotape Recording ,Middle Aged ,medicine.disease ,Sensory Systems ,Visual field ,Ophthalmology ,Visual field test ,Fixation (visual) ,Female ,Visual Fields ,business ,Scientific Correspondence - Abstract
Aims: To evaluate the effect of a visual field test educational video on the reliability of the first automated visual field test of new patients. Methods: A prospective, randomised, controlled trial of an educational video on visual field test reliability of patients referred to the hospital eye service for suspected glaucoma was undertaken. Patients were randomised to either watch an educational video or a control group with no video. The video group was shown a 4.5 minute audiovisual presentation to familiarise them with the various aspects of visual field examination with particular emphasis on sources of unreliability. Reliability was determined using standard criteria of fixation loss rate less than 20%, false positive responses less than 33%, and false negative responses less than 33%. Results: 244 patients were recruited; 112 in the video group and 132 in the control group with no significant between group difference in age, sex, and density of field defects. A significant improvement in reliability (p=0.015) was observed in the group exposed to the video with 85 (75.9%) patients having reliable results compared to 81 (61.4%) in the control group. The difference was not significant for the right (first tested) eye with 93 (83.0%) of the visual fields reliable in the video group compared to 106 (80.0%) in the control group (p = 0.583), but was significant for the left (second tested) eye with 97 (86.6 %) of the video group reliable versus 97 (73.5%) of the control group (p = 0.011). Conclusions: The use of a brief, audiovisual patient information guide on taking the visual field test produced an improvement in patient reliability for individuals tested for the first time. In this trial the use of the video had most of its impact by reducing the number of unreliable fields from the second tested eye.
- Published
- 2003
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